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@@ -2,16 +2,98 @@
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/**
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* @file
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- * JBrowse Instance page
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+ * Bartik's theme implementation to display a node.
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*
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* Available variables:
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- * - url_prefix: the URL without parameters for the JBrowse to be embedded.
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- * - location: the location to display by default
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- * - tracks: a comma-separated list of tracks to display by default
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- * - url: the full URL for the JBrowse you would like to embed
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+ * - $title: the (sanitized) title of the node.
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+ * - $content: An array of node items. Use render($content) to print them all,
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+ * or print a subset such as render($content['field_example']). Use
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+ * hide($content['field_example']) to temporarily suppress the printing of a
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+ * given element.
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+ * - $user_picture: The node author's picture from user-picture.tpl.php.
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+ * - $date: Formatted creation date. Preprocess functions can reformat it by
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+ * calling format_date() with the desired parameters on the $created variable.
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+ * - $name: Themed username of node author output from theme_username().
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+ * - $node_url: Direct URL of the current node.
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+ * - $display_submitted: Whether submission information should be displayed.
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+ * - $submitted: Submission information created from $name and $date during
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+ * template_preprocess_node().
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+ * - $classes: String of classes that can be used to style contextually through
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+ * CSS. It can be manipulated through the variable $classes_array from
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+ * preprocess functions. The default values can be one or more of the
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+ * following:
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+ * - node: The current template type; for example, "theming hook".
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+ * - node-[type]: The current node type. For example, if the node is a
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+ * "Blog entry" it would result in "node-blog". Note that the machine
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+ * name will often be in a short form of the human readable label.
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+ * - node-teaser: Nodes in teaser form.
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+ * - node-preview: Nodes in preview mode.
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+ * The following are controlled through the node publishing options.
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+ * - node-promoted: Nodes promoted to the front page.
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+ * - node-sticky: Nodes ordered above other non-sticky nodes in teaser
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+ * listings.
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+ * - node-unpublished: Unpublished nodes visible only to administrators.
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+ * - $title_prefix (array): An array containing additional output populated by
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+ * modules, intended to be displayed in front of the main title tag that
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+ * appears in the template.
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+ * - $title_suffix (array): An array containing additional output populated by
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+ * modules, intended to be displayed after the main title tag that appears in
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+ * the template.
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+ *
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+ * Other variables:
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+ * - $node: Full node object. Contains data that may not be safe.
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+ * - $type: Node type; for example, story, page, blog, etc.
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+ * - $comment_count: Number of comments attached to the node.
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+ * - $uid: User ID of the node author.
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+ * - $created: Time the node was published formatted in Unix timestamp.
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+ * - $classes_array: Array of html class attribute values. It is flattened
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+ * into a string within the variable $classes.
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+ * - $zebra: Outputs either "even" or "odd". Useful for zebra striping in
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+ * teaser listings.
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+ * - $id: Position of the node. Increments each time it's output.
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+ *
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+ * Node status variables:
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+ * - $view_mode: View mode; for example, "full", "teaser".
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+ * - $teaser: Flag for the teaser state (shortcut for $view_mode == 'teaser').
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+ * - $page: Flag for the full page state.
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+ * - $promote: Flag for front page promotion state.
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+ * - $sticky: Flags for sticky post setting.
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+ * - $status: Flag for published status.
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+ * - $comment: State of comment settings for the node.
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+ * - $readmore: Flags true if the teaser content of the node cannot hold the
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+ * main body content.
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+ * - $is_front: Flags true when presented in the front page.
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+ * - $logged_in: Flags true when the current user is a logged-in member.
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+ * - $is_admin: Flags true when the current user is an administrator.
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+ *
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+ * Field variables: for each field instance attached to the node a corresponding
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+ * variable is defined; for example, $node->body becomes $body. When needing to
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+ * access a field's raw values, developers/themers are strongly encouraged to
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+ * use these variables. Otherwise they will have to explicitly specify the
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+ * desired field language; for example, $node->body['en'], thus overriding any
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+ * language negotiation rule that was previously applied.
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+ *
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+ * @see template_preprocess()
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+ * @see template_preprocess_node()
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+ * @see template_process()
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*/
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?>
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+<?php
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+ // Determine the URL of the JBrowse based on the node properties
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+ $url = $node->field_jburl['und'][0]['url'];
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+ $location = (!empty($node->field_jbloc)) ? $node->field_jbloc['und'][0]['safe_value'] : '';
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+ $tracks = (!empty($node->field_jbtracks)) ? $node->field_jbtracks['und'][0]['safe_value'] : '';
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+
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+ $url = "$url/?q=loc=$location&tracks=$tracks";
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+?>
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+
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+<style>
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+iframe {
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+ min-height: 600px;
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+}
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+</style>
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+
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<div id="node-<?php print $node->nid; ?>" class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
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<?php if (!$page): ?>
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@@ -22,12 +104,10 @@
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<?php print render($title_suffix); ?>
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<div class="content clearfix"<?php print $content_attributes; ?>>
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- <div class="jbrowse" id="GenomeBrowser">
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- <div id="LoadingScreen" style="padding: 50px;">
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- <h1>Loading...</h1>
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- </div>
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+ <div id="JBrowseInstance">
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+ <iframe src="<?php print $url;?>" width="100%" height="100%">
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+ </iframe>
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</div>
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- <div style="display: none">JBrowseDefaultMainPage</div>
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</div>
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</div>
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Lacey Sanderson